What's the difference between pipe and RYO tobacco?

Mainly the cut. I've rolled pipe tobacco, of course, but it usually doesn't smoke so well wrapped in paper because the cut is too coarse and the type of tobacco used for pipes is usually too strong for cigarettes. You might do well to ask a tobacco store and they can explain if there's a difference in type as well. You have to be as careful with pipe tobacco as with cigarette tobacco, by the way: make sure it's not full of some kind of flavoring that might be artificial and deadly. Pipe tobacco is generally meant to be only puffed, not inhaled. Your best bet is to ask a pro about this.
In the meantime, do a search on growing your own and learning how to cure it. That's the only way to know for sure what you're smoking.

i've looked into a few websites, but can anyone recommend a high quality site and quality tobaccos?

I order from Customblends.com, very good high quality tobacco.

does anyone know where to get bourbon or whiskey flavored cigarette roll your own tobacco

i just ordered some whiskey flavored pipe tobacco from www.pipesandcigars.com Peter Stokkebye Bulk bend. i also read recently that "smooth" and "english" varities of pipe tobacco are closer to what a cigarette smoker is looking for.

Rollyourown.com is the best I have found.